On 9/2/13 9:43 PM, Jernej Zidar wrote:
Dear Justin,
I set the couple_intramol parameter to yes and rerun the free energy
simulations. mdrun was able to fully utilize all the cores in the
system but there's one issue. The free energy of solvation is vastly
different if the parameter is set to 'no' (DG=-408.10 +/- 8.69 kJ/mol)
or 'yes' (1890.14 +/- 15.52).
The behavior observed in the simulations is more consistent with the
latter number.
The latter number, of course, is not an actual final answer. You have to do a
corresponding gas-phase calculation to determine the real DG of solvation.
The manual states that 'yes' can be used can be "useful for
partitioning free-energies of relatively large molecules, where the
intra-molecular non-bonded interactions might lead to kinetically
trapped vacuum conformations. The 1-4 pair interactions are not turned
off."
My molecule has 161 atoms. How large is "relatively large" ?
I think a bigger factor is flexibility. For a relatively rigid, conjugated
system, it may not be a big issue. Gut feeling? Yes, I'd say that something
with 161 atoms is relatively large.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
